Molecular Cell Biology

Research Output

2020

Accumulation of Nickel by Excluder Thlaspi arvense and Hyperaccumulator Noccaea caerulescens upon Short-Term and Long-Term Exposure

Kozhevnikova, A. D., Seregin, I. V. & Schat, H., Mar 2020, In : Russian Journal of Plant Physiology. 67, 2, p. 303-311 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Acetylene containing cyclo(L-Tyr-L-Tyr)-analogs as mechanism-based inhibitors of CYP121A1 from Mycobacterium tuberculosis

Ortega Ugalde, S., Wallraven, K., Speer, A., Bitter, W., Grossmann, T. N. & Commandeur, J. N. M., 26 Mar 2020, (Accepted/In press) In : Biochemical Pharmacology. 177, 47 p., 113938.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A Chimeric EccB-MycP Fusion Protein is Functional and a Stable Component of the ESX-5 Type VII Secretion System Membrane Complex

van Winden, V. J. C., Bunduc, C. M., Ummels, R., Bitter, W. & Houben, E. N. G., 14 Feb 2020, In : Journal of Molecular Biology. 432, 4, p. 1265-1278

Research output: Contribution to JournalArticleAcademicpeer-review

A combined experimental and modelling approach for the Weimberg pathway optimisation

Shen, L., Kohlhaas, M., Enoki, J., Meier, R., Schönenberger, B., Wohlgemuth, R., Kourist, R., Niemeyer, F., van Niekerk, D., Bräsen, C., Niemeyer, J., Snoep, J. & Siebers, B., 27 Feb 2020, In : Nature Communications. 11, 1, p. 1-13 13 p., 1098.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A dynamic energy budget model for small yellow croaker Larimichthys polyactis: Parameterisation and application in its main geographic distribution waters

Ren, J. S., Jin, X., Yang, T., Kooijman, S. A. L. M. & Shan, X., 29 Apr 2020, In : Ecological Modelling. 427, p. 1-8 8 p., 109051.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Aflatoxins: Occurrence, exposure, and binding to lactobacillus species from the gut microbiota of rural ugandan children

Wacoo, A. P., Atukunda, P., Muhoozi, G., Braster, M., Wagner, M., van den Broek, T. J., Sybesma, W., Westerberg, A. C., Iversen, P. O. & Kort, R., Mar 2020, In : Microorganisms. 8, 3, p. 1-15 15 p., 347.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Analysis of a predator–prey model with specific time scales:a geometrical approach proving the occurrence of canard solutions

Poggiale, J. C., Aldebert, C., Girardot, B. & Kooi, B. W., 2020, In : Journal of Mathematical Biology. 80, 1-2, p. 39-60 21 p.

Research output: Contribution to JournalArticleAcademicpeer-review

A new target for an old enemy: The Cytochrome P450 system from Mycobacterium tuberculosis

Ortega Ugalde, S., 2020, 204 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VU

Open Access
File

An Improved ATP FRET Sensor for Yeast Shows Heterogeneity during Nutrient Transitions

Botman, D., Van Heerden, J. H. & Teusink, B., 27 Mar 2020, In : ACS Sensors. 5, 3, p. 814-822 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae

Garcia-Albornoz, M., Holman, S. W., Antonisse, T., Daran-Lapujade, P., Teusink, B., Beynon, R. J. & Hubbard, S. J., Feb 2020, In : Molecular Omics. 16, 1, p. 59-72 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A safe harbor can protect an endangered species from its predators

Banerjee, M., Kooi, B. & Venturino, E., 2020, (Accepted/In press) In : Ricerche di Matematica.

Research output: Contribution to JournalArticleAcademicpeer-review

Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs

Mondeel, T. D. G. A., Ivanov, O., Westerhoff, H. V., Liebermeister, W. & Barberis, M., 3 Apr 2020, In : NPJ systems biology and applications. 6, 1, p. 1-15 15 p., 8.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity

Abudukelimu, A., Barberis, M., Redegeld, F., Sahin, N., Sharma, R. P. & Westerhoff, H. V., 14 Feb 2020, In : Frontiers in Immunology. 10, p. 1-20 20 p., 3091.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Current Trends in Dynamical Systems in Biology and Natural Sciences

Aguiar, M. (ed.), Braumann, C. (ed.), Kooi, B. (ed.), Pugliese, A. (ed.) & Stollenwerk, N. (ed.), 21 Jun 2020, (Accepted/In press) Springer. (SEMA SIMAI Springer Series; vol. 21)

Research output: Book / ReportBook editingAcademic

Development and evaluation of a harmonized whole body physiologically based pharmacokinetic (PBPK) model for flutamide in rats and its extrapolation to humans

Sharma, R. P., Kumar, V., Schuhmacher, M., Kolodkin, A. & Westerhoff, H. V., 1 Mar 2020, In : Environmental Research. 182, p. 1-14 14 p., 108948.

Research output: Contribution to JournalArticleAcademicpeer-review

Development of a high-throughput bioassay for screening of antibiotics in aquatic environmental samples

Jonkers, T. J. H., Steenhuis, M., Schalkwijk, L., Luirink, J., Bald, D., Houtman, C. J., Kool, J., Lamoree, M. H. & Hamers, T., 28 Apr 2020, In : Science of the Total Environment. 729, p. 1-9 9 p., 139028.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Elementary Growth Modes provide a molecular description of cellular self-fabrication

de Groot, D. H., Hulshof, J., Teusink, B., Bruggeman, F. J. & Planqué, R., 1 Jan 2020, In : PLoS Computational Biology. 16, 1, e1007559.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Fermented foods in a global age: East meets West

Tamang, J. P., Cotter, P. D., Endo, A., Han, N. S., Kort, R., Liu, S. Q., Mayo, B., Westerik, N. & Hutkins, R., 3 Jan 2020, In : Comprehensive Reviews in Food Science and Food Safety. 19, 1, p. 184-217 34 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Long-term exposure of activated sludge in chemostats leads to changes in microbial communities composition and enhanced biodegradation of 4-chloroaniline and N-methylpiperazine

Poursat, B. A. J., van Spanning, R. J. M., Braster, M., Helmus, R., de Voogt, P. & Parsons, J. R., 1 Mar 2020, In : Chemosphere. 242, 125102.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

MEMOTE for standardized genome-scale metabolic model testing

Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert, B. E., Edirisinghe, J. N., Faria, J. P., Feist, A. M., Fengos, G., Fleming, R. M. T., García-Jiménez, B., Hatzimanikatis, V. & 49 others, van Helvoirt, W., Henry, C. S., Hermjakob, H., Herrgård, M. J., Kaafarani, A., Kim, H. U., King, Z., Klamt, S., Klipp, E., Koehorst, J. J., König, M., Lakshmanan, M., Lee, D. Y., Lee, S. Y., Lee, S., Lewis, N. E., Liu, F., Ma, H., Machado, D., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G. L., Monk, J. M., Nielsen, J., Nielsen, L. K., Nogales, J., Nookaew, I., Palsson, B. O., Papin, J. A., Patil, K. R., Poolman, M., Price, N. D., Resendis-Antonio, O., Richelle, A., Rocha, I., Sánchez, B. J., Schaap, P. J., Malik Sheriff, R. S., Shoaie, S., Sonnenschein, N., Teusink, B., Vilaça, P., Vik, J. O., Wodke, J. A. H., Xavier, J. C., Yuan, Q., Zakhartsev, M. & Zhang, C., 1 Mar 2020, In : Nature Biotechnology. 38, 3, p. 272-276 5 p.

Research output: Contribution to JournalLetterAcademicpeer-review

Open Access

Microdroplet screening and selection for improved microbial production of extracellular compounds

van Tatenhove-Pel, R. J., Hernandez-Valdes, J. A., Teusink, B., Kuipers, O. P., Fischlechner, M. & Bachmann, H., Feb 2020, In : Current Opinion in Biotechnology. 61, p. 72-81 10 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access

Modification of a PE/PPE substrate pair reroutes an Esx substrate pair from the mycobacterial ESX-1 type VII secretion system to the ESX-5 system

Damen, M. P. M., Phan, T. H., Ummels, R., Rubio-Canalejas, A., Bitter, W. & Houben, E. N. G., 17 Mar 2020, In : Journal of Biological Chemistry. 295, 18, p. 5960-5969

Research output: Contribution to JournalArticleAcademicpeer-review

Mutagenesis-Based Characterization and Improvement of a Novel Inclusion Body Tag

Jong, W. S. P., ten Hagen-Jongman, C. M., Vikström, D., Dontje, W., Abdallah, A. M., de Gier, J. W., Bitter, W. & Luirink, J., 10 Jan 2020, In : Frontiers in Bioengineering and Biotechnology. 7, 442.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing (Nature Biotechnology, (2020), 38, 3, (272-276), 10.1038/s41587-020-0446-y)

Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., Diener, C., Dräger, A., Ebert, B. E., Edirisinghe, J. N., Faria, J. P., Feist, A. M., Fengos, G., Fleming, R. M. T., García-Jiménez, B., Hatzimanikatis, V. & 49 others, van Helvoirt, W., Henry, C. S., Hermjakob, H., Herrgård, M. J., Kaafarani, A., Kim, H. U., King, Z., Klamt, S., Klipp, E., Koehorst, J. J., König, M., Lakshmanan, M., Lee, D. Y., Lee, S. Y., Lee, S., Lewis, N. E., Liu, F., Ma, H., Machado, D., Mahadevan, R., Maia, P., Mardinoglu, A., Medlock, G. L., Monk, J. M., Nielsen, J., Nielsen, L. K., Nogales, J., Nookaew, I., Palsson, B. O., Papin, J. A., Patil, K. R., Poolman, M., Price, N. D., Resendis-Antonio, O., Richelle, A., Rocha, I., Sánchez, B. J., Schaap, P. J., Sheriff, R. S. M., Shoaie, S., Sonnenschein, N., Teusink, B., Vilaça, P., Vik, J. O., Wodke, J. A. H., Xavier, J. C., Yuan, Q., Zakhartsev, M. & Zhang, C., 1 Apr 2020, In : Nature Biotechnology. 38, 4, p. 1-1 1 p.

Research output: Contribution to JournalErratumAcademic

Open Access

Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis

Nilsson, A., Haanstra, J. R., Engqvist, M., Gerding, A., Bakker, B. M., Klingmüller, U., Teusink, B. & Nielsen, J., 12 May 2020, In : Proceedings of the National Academy of Sciences of the United States of America. 117, 19, p. 10294-10304 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Sensing Extracellular Calcium – An Insight into the Structure and Function of the Calcium-Sensing Receptor (CaSR)

Chavez-Abiega, S., Mos, I., Centeno, P. P., Elajnaf, T., Schlattl, W., Ward, D. T., Goedhart, J. & Kallay, E., 2020, Calcium Signaling. Islam, S. (ed.). 2nd ed. Cham: Springer Nature Switzerland AG, p. 1031-1063 33 p. (Advances in Experimental Medicine and Biology; vol. 1131).

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Single molecule mRNA fluorescent in situ hybridization combined with immunofluorescence in S. cerevisiae: Dataset and quantification

Maekiniemi, A., Singer, R. H. & Tutucci, E., 11 Apr 2020, In : Data in brief. 30, p. 1-11 11 p., 105511.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

The carboxy-terminal insert in the Q-loop is needed for functionality of Escherichia coli cytochrome bd-I

Ghasemi Goojani, H. A., Konings, J., Hakvoort, H., Hong, S., Gennis, R. B., Sakamoto, J., Lill, H. & Bald, D., 12 Feb 2020, In : Biochimica et Biophysica Acta - Bioenergetics. 1861, 5-6, p. 1-10 10 p., 148175.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

The comparative energetics of petrels and penguins

Kooijman, S. A. L. M., 1 May 2020, In : Ecological Modelling. 427, p. 1-8 8 p., 109052.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

The energetic basis of population growth in animal kingdom

Kooijman, S. A. L. M., Lika, K., Augustine, S., Marn, N. & Kooi, B. W., 15 May 2020, In : Ecological Modelling. 428, p. 1-15 15 p., 109055.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

The standard dynamic energy budget model has no plausible alternatives

Kooijman, S. A. L. M., 11 May 2020, In : Ecological Modelling. 428, p. 1-5 5 p., 109106.

Research output: Contribution to JournalArticleAcademicpeer-review

The use of augmented loss functions for estimating dynamic energy budget parameters

Lika, K., Augustine, S. & Kooijman, S. A. L. M., 18 May 2020, In : Ecological Modelling. 428, p. 1-8 8 p., 109110.

Research output: Contribution to JournalArticleAcademicpeer-review

Transthyretin-binding activity of complex mixtures representing the composition of thyroid-hormone disrupting contaminants in house dust and human serum

Hamers, T., Kortenkamp, A., Scholze, M., Molenaar, D., Cenijn, P. H. & Weiss, J. M., 31 Jan 2020, In : Environmental Health Perspectives. 128, 1, p. 1-15 15 p., 017015.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Trumping the Trumps: Addressing complexities through BioLogical rationality

Westerhoff, H. V., 17 Jan 2020, Amsterdam: Vrije Universiteit Amsterdam. 37 p.

Research output: Book / ReportValedictory speechProfessional

Open Access
File
2019

Acetogenins: Chemoenzymatic synthesis and molecular probing of respiratory NADH-dehydrogenases

van Lint, M., 2019, 326 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VU

Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength

Price, C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F. J., Marrink, S. J., Montalban-Lopez, M., De Jong, A., Kok, J., Molenaar, D., Poolman, B., Teusink, B. & Kuipers, O. P., 10 Jan 2019, In : BMC Evolutionary Biology. 19, 1, p. 1-15 15 p., 15.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris

Özcan, E., Selvi, S. S., Nikerel, E., Teusink, B., Toksoy Öner, E. & Çakır, T., 1 Jan 2019, In : Applied Microbiology and Biotechnology. 103, 7, p. 3153-3165 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Altricial-precocial spectra in animal kingdom

Augustine, S., Lika, K. & Kooijman, S. A. L. M., Jan 2019, In : Journal of sea research. 143, p. 27-34 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Ampicillin-treated Lactococcus lactis MG1363 populations contain persisters as well as viable but non-culturable cells

van Tatenhove-Pel, R. J., Zwering, E., Solopova, A., Kuipers, O. P. & Bachmann, H., 1 Dec 2019, In : Scientific Reports. 9, 1, 9867.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Ample arsenite bio-oxidation activity in Bangladesh drinking water wells: A bonanza for bioremediation?

Hassan, Z., Sultana, M., Khan, S. I., Braster, M., Röling, W. F. M. & Westerhoff, H. V., Aug 2019, In : Microorganisms. 7, 8, p. 1-22 22 p., 246.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Analysis of Arabidopsis thaliana HKT1 and Eutrema salsugineum/botschantzevii HKT1;2 Promoters in Response to Salt Stress in Athkt1:1 Mutant

Nawaz, I., Iqbal, M., Hakvoort, H. W. J., de Boer, A. H. & Schat, H., 1 Jun 2019, In : Molecular Biotechnology. 61, 6, p. 442-450 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A new phase in DEB research

Augustine, S. & Kooijman, S. A. L. M., Jan 2019, In : Journal of sea research. 143, p. 1-7 7 p.

Research output: Contribution to JournalEditorialAcademicpeer-review

A Photoswitchable Agonist for the Histamine H 3 Receptor, a Prototypic Family A G-Protein-Coupled Receptor

Hauwert, N. J., Mocking, T. A. M., Da Costa Pereira, D., Lion, K., Huppelschoten, Y., Vischer, H. F., De Esch, I. J. P., Wijtmans, M. & Leurs, R., 26 Mar 2019, In : Angewandte Chemie - International Edition. 58, 14, p. 4531-4535 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A systematic assessment of current genome-scale metabolic reconstruction tools

Mendoza, S. N., Olivier, B. G., Molenaar, D. & Teusink, B., 7 Aug 2019, In : Genome Biology. 20, 1, 158.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal

Groenenboom, A. E., Parker, M. E., De Vries, A., De Groot, S., Zobrist, S., Mansen, K., Milani, P., Kort, R., Smid, E. J. & Schoustra, S. E., 10 May 2019, In : PLoS ONE. 14, 5, e0215658.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Bacterial inclusion bodies function as vehicles for dendritic cell-mediated T cell responses

Schetters, S. T. T., Jong, W., Kruijssen, L. J. W., van den Berg van Saparoea, B., Engels, S., Unger, W. W. J., Houben, D., den Haan, J. M. M., Luirink, J. & van Kooyk, Y., 8 Oct 2019, In : cellular & molecular immunology. 17, 4, p. 415-417 3 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Biodegradation of metformin and its transformation product, guanylurea, by natural and exposed microbial communities

Poursat, B. A. J., van Spanning, R. J. M., Braster, M., Helmus, R., de Voogt, P. & Parsons, J. R., 30 Oct 2019, In : Ecotoxicology and Environmental Safety. 182, p. 1-10 10 p., 109414.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Body size as emergent property of metabolism

Lika, K., Augustine, S. & Kooijman, S. A. L. M., Jan 2019, In : Journal of sea research. 143, p. 8-17 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Chaperones and substrate specificity, type VII secretion systems reconnected

Phan, T. H., 2019, 194 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VU

Open Access
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